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- PDB-5myw: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -

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Basic information

Entry
Database: PDB / ID: 5myw
TitleStructure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound SB-435634 at 1.77A resolution
ComponentsHTH-type transcriptional regulator EthR
KeywordsTRANSCRIPTION / EthR / Mycobacterium tuberculosis / represor
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytosol
Similarity search - Function
: / Transcriptional regulator EthR, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily ...: / Transcriptional regulator EthR, C-terminal domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
~{N}2-(1,3-benzodioxol-5-yl)benzene-1,2-diamine / HTH-type transcriptional regulator EthR
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBlaszczyk, M. / Mendes, V. / Mugumbate, G. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Front Pharmacol / Year: 2017
Title: Target Identification of Mycobacterium tuberculosis Phenotypic Hits Using a Concerted Chemogenomic, Biophysical, and Structural Approach.
Authors: Mugumbate, G. / Mendes, V. / Blaszczyk, M. / Sabbah, M. / Papadatos, G. / Lelievre, J. / Ballell, L. / Barros, D. / Abell, C. / Blundell, T.L. / Overington, J.P.
History
DepositionJan 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4882
Polymers25,2591
Non-polymers2281
Water1,18966
1
A: HTH-type transcriptional regulator EthR
hetero molecules

A: HTH-type transcriptional regulator EthR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9754
Polymers50,5192
Non-polymers4562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2750 Å2
ΔGint-21 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.528, 121.528, 33.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#1: Protein HTH-type transcriptional regulator EthR


Mass: 25259.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WMC1
#2: Chemical ChemComp-WCU / ~{N}2-(1,3-benzodioxol-5-yl)benzene-1,2-diamine


Mass: 228.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.7 to 2.1 ammonium sulfate 0.1M MES (pH 6 to 7) 5 to 15%(v/v) glycerol 7 to 12%(v/v) 1,4-dioxane
PH range: pH range 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→60.764 Å / Num. all: 25356 / Num. obs: 25356 / % possible obs: 99.7 % / Redundancy: 12.5 % / Biso Wilson estimate: 32.05 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.083 / Rsym value: 0.077 / Net I/av σ(I): 5.7 / Net I/σ(I): 19.1 / Num. measured all: 316819
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.77-1.8612.91.340.60.3941.4371.3499.5
1.86-1.98130.7710.2280.8260.7799.4
1.98-2.1112.50.41.80.120.4290.499.5
2.11-2.2813.20.2462.90.0710.2620.24699.9
2.28-2.512.40.1494.90.0450.160.14999.9
2.5-2.812.90.1017.10.030.1090.101100
2.8-3.2312.10.0739.30.0230.0790.073100
3.23-3.9511.90.05610.80.0170.0610.056100
3.95-5.59110.0512.10.0160.0540.05100
5.59-60.76410.40.03913.60.0130.0420.03999.8

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T56

1t56


Resolution: 1.77→33.706 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.98
RfactorNum. reflection% reflection
Rfree0.1983 1291 5.1 %
Rwork0.1762 --
obs0.1773 25300 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.32 Å2 / Biso mean: 47.1954 Å2 / Biso min: 19.96 Å2
Refinement stepCycle: final / Resolution: 1.77→33.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 17 66 1566
Biso mean--67.02 50.38 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061533
X-RAY DIFFRACTIONf_angle_d0.7612093
X-RAY DIFFRACTIONf_chiral_restr0.047241
X-RAY DIFFRACTIONf_plane_restr0.006271
X-RAY DIFFRACTIONf_dihedral_angle_d13.265904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7683-1.83910.2851730.26312558273199
1.8391-1.92280.2821500.23772584273499
1.9228-2.02420.24351350.20282626276199
2.0242-2.1510.23721230.178726362759100
2.151-2.3170.18761500.174626372787100
2.317-2.55010.21281470.17226542801100
2.5501-2.91890.21941420.182826852827100
2.9189-3.67680.21011210.17627502871100
3.6768-33.71190.16231500.162528793029100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.4163-4.73721.53739.3175-3.76652.17870.04840.5595-0.362-1.15060.08860.70130.3711-0.0514-0.02440.5838-0.1453-0.06150.3853-0.00540.4281-24.8293-50.5238-6.2868
23.22851.5811-2.36997.0892-0.04485.8847-0.11910.19370.4784-0.27180.29090.8747-0.80870.2044-0.24630.6173-0.19540.06510.33050.03370.4575-28.6625-58.5687-1.1711
34.32415.88712.65317.93983.54063.55440.6142-0.1423-0.10560.928-0.33930.08120.9920.0119-0.330.53610.04360.01450.25460.04630.3548-14.6134-41.57243.3181
40.44721.37210.31636.9005-0.79391.37730.7287-0.4410.74950.18120.1802-0.8366-0.55271.1194-0.68570.7074-0.00670.41131.0971-0.03691.70344.4298-26.5880.4953
58.98373.32210.12877.77671.76923.6396-0.0040.17770.1335-0.0180.17510.04260.36530.0723-0.15360.33260.06120.00530.18980.04380.2065-13.6845-31.6523-3.1081
64.35343.9987-0.15529.6051.10774.2006-0.065-0.3829-0.21550.426-0.0506-0.15770.40930.18650.09030.26370.10930.01420.24730.0290.1882-13.2451-26.03359.8875
72.88480.40031.15262.72810.80055.24070.07270.1671-0.071-0.1148-0.05840.04760.234-0.0537-0.00440.23230.07570.00220.242-0.00140.2479-16.1442-22.2306-2.7567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 46 )A22 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 67 )A47 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 92 )A68 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 98 )A93 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 128 )A99 - 128
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 167 )A129 - 167
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 214 )A168 - 214

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